'''
Created on Mar 3, 2011

@author: oabalbin
'''
'''
    Annotate both hard threshold and model based called snps
    # Hard Filtering
    commandA = ann.create_snps_annotation(snps_hard_vcf, snps_hard_annotated_vcf, 
                            snps_hard_annotated_log, vcfCodSNP_genome, 
                            genelist_annotation, path_to_vcfCodSNPs)
    
    commandB = ann.create_snps_annotation(snps_model_vcf, snps_model_annotated_vcf, 
                            snps_model_annotated_log, vcfCodSNP_genome, 
                            genelist_annotation, path_to_vcfCodSNPs)
    
    
    command = commandA+'\n'+commandB
    
    jobidann = jobrunfunc(jobn+'_ann', command, SINGLE_CORE, cwd=None, walltime=WT_SHORT, pmem=extra_mem, 
                              deps=[jobidtc,jobidhf], stdout=None, email_addresses=my_email)
    
    # files for config file
    analysis.snps_hard_annotated_vcf
    analysis.snps_hard_annotated_log
    analysis.snps_model_annotated_vcf
    analysis.snps_model_annotated_log
    ....
    vcfCodSNP_genome
    path_to_vcfCodSNPs
    genelist_annotations
    
'''
